Background: Neonatal death accounts for one fifth of all under-five mortality in Uganda. Suboptimal newborn care practices resulting from hypothermia, poor hygiene and delayed initiation of breastfeeding are leading predisposing factors. Evidence suggests focused educational prenatal care messages to mitigate these problems. However, there is a paucity of data on the interaction between the service provider and the prenatal service user. This study aims to understand the scope of educational information and current practices on newborn care from the perspectives of prenatal mothers and health workers. Methods: A qualitative descriptive methodology was used. In-depth interviews were conducted with lactating mothers (n = 31) of babies younger than five months old across Masindi in western Uganda. Additional interviews with health workers (n = 17) and their employers or trainers (n = 5) were conducted to strengthen our findings. Data were audio-taped and transcribed verbatim. A thematic content analysis was performed using NVivo 8. Results: Vertical programmes received more attention than education for newborn care during prenatal sessions. In addition, attitudinal and communication problems existed among health workers thereby largely ignoring the fundamental principles of patient autonomy and patient-centred care. The current newborn care practices were largely influenced by relatives' cultural beliefs rather than by information provided during prenatal sessions. There is a variation in the training curriculum for health workers deployed to offer recommended prenatal and immediate newborn care in the different tiers of health care. Conclusions: Findings revealed serious deficiencies in prenatal care organisations in Masindi. Pregnant mothers remain inadequately prepared for childbirth and newborn care, despite their initiative to follow prenatal sessions. These findings call for realignment of prenatal care by integrating education on newborn care practices into routine antenatal care services and be based on principles of patient-centred care.